I noticed that after you annex an enemy empire the AI tend to scrap the extra ships, specially in private sector. The thing is that each ship give a tech bonus, even if that ship is totally low tech and that greatly bump the player, a clearly exploit.

I disagree that it's an exploit. The scrapping of civilian ships is entirely outside the control of the player, and one cannot exploit this behaviour. Also, the bonuses gleaned from the scrapping of civilian ships applies equally if one computer controlled position takes over another.

But I agree - scrapping of civilian ships should be excluded from tech bonuses.